The show starts back in ancient times, on a battlefield, with Ra’s al Ghul getting brought back from the dead. Ra’s is given dagger and told to find his heir so that he can be free.
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In present day Gotham, Bruce looks out over the docks. Along with Aflred, Bruce is trying to stop a shipment coming in from Penguin. After getting surrounded by thugs, Bruce beats his way out of trouble. Selina was also there, in a mask, trying to steal something but Bruce stopped her.
Jim is out in the countryside, arriving at Falcone’s mansion to meet him. He is introduced to Falcone’s daughter, Sofia. Bruce tells Carmine that he needs his help taking Gotham back from Penguin, but Falcone says that he can’t because he’s dying. Sofia volunteers to go back to Gotham in his stead.
Back in Gotham, Bruce tells Alfred that he has to back to the docks. It’s his chance to investigate a real crime and stop something bad before it happens.
Barbara is doing a weapons demonstration for a bunch of criminals at her new clubhouse. Selina returns but doesn’t have the crate from Penguin’s shipment. Barbara will do it herself. At Penguin’s club, he orders Zsasz to take him to the new shipment. When they leave, a woman enters the club and begins to unfreeze Riddler.
Later, Penguin returns to the club to find Ridddler gone. Elsewhere, the woman wakes him up. She has an obsession with the Riddler, she’s Myrtle Jenkins, his number one fan. Myrtle tells Riddler he’s been frozen for five months, showing him a picture of the club. She’s going to help him become Gotham’s greatest villain as long as she can be his sidekick.
Bruce arrives at the dock dressed as a normal teenager, asking for work. He finds a notebook in the ship that brought Penguin’s stuff in and the men confront him. Alfred shows up to save the day again.
Barbara and Penguin are talking about his auction that’s taking place, and she says that she wants to buy a specific knife from his inventory. It’s for a “client.” Penguin declines and tells her he’ll see her at the auction. When she leaves, Penguin pulls out R’as al Ghul’s knife.
Bruce and Alfred are talking about the same knife since it was on the manifesto. They connect it to al Ghul and realize he’s been alive for two thousand years.
At Falcone’s, Sofia talks to Jim about her dad and their relationship. Jim apologizes for killing her brother but Sofia understands. On the beach, Sofia kisses Jim.
Zsasz is explaining to Penguin that Riddler is nowhere in Gotham. Meanwhile, Nygma wakes up to Myrtle being crazy about his persona. She says that it took months to plan his escape and Riddler is impressed. He’s struggling to think of new puzzles and doesn’t seem like himself.
Bruce and Alfred get ready for Penguin’s auction so they can investigate the auction. At the auction, Bruce acts like a billionaire brat, just as Alfred advised. Penguin and Barbara both arrive in time for the knife auction. Bruce and Barbara get into a bidding war over the knife until Bruce wins by putting up $2 million. Penguin tells Bruce to watch out because Barbara will be coming for him.
Myrtle is upset with Nygma because he can’t even solve children’s riddles. He surprises her by showing that he can move and knocking her out cold.
Selina breaks into Wayne Manor to try and find the knife but Bruce was already waiting. Selina tries to convince him to give up the knife, and she tells Bruce about her troubles. He apologizes and says she should go. Bruce pulls the knife out after she leaves hoping al Ghul will show up.
Harvey introduces Jim to a new detective at GCPD. Sofia arrives at the station to see Jim and tells him that she came back to Gotham to help him.
Penguin confronts Myrtle and she tells him that his mind isn’t working any more. He tells Zsasz to make an example of Myrtle and he kills her. Nygma, meanwhile, is walking the streets of Gotham.
Ra’s al Ghul appears to Barbara and they fight because she doesn’t have the knife. She tells Ra’s that Bruce has the knife instead and he’s not angry anymore. He tells her that the knife is the key to everything and the two begin to kiss.
The end.